Scientific writing can extend beyond LaTeX, made possible by formats,
such as
Markdown (and its many flavours),
reStructuredText and
Jupyter notebooks.
:bookmark: means ability to seamlessly cite references.
:link: means ability to cross-reference figures and sections within the
document.
Markdown text editor.
IDE for R.
Command line text editor.
Popular IDE with Markdown support.
Markdown editor which
Crowdsourced
Open source bibliography reference manager.
FOSS tool to collect, organize, cite, and
Online bibliography reference manager.
Reference managers to generate citations, BibTeX, and BibLaTeX files.
repository with over 9000 free CSL citation styles and an online
editor to create new ones.
share research.
Open source, online, desktop and
Visualization software for graphs and
Define simple diagrams instead of drawing them.
Define charts and more complex diagrams.
Define UML diagrams instead of drawing them.
Drawing illustrations themselves has driven many a scientist mad. Fortunately,
there are formal languages with which one can create beautiful graphics.
container deployable diagramming software named draw.io.
networks which uses a domain-specific DOT language.
Python package which renders HTML presentations
Python package which can
A static site generator which converts
Markedly Structured Text,
Convert Jupyter
Haskell library for converting from
Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia :bookmark: :link:.
Supplementary files and tools.
from Markdown source using remark or reveal.js :link:.
convert reStructuredText into various formats and provides command-line
tools to do it :link:.
a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website.
a superset of CommonMark markdown with reStructuredText like features.
notebooks into reveal.js presentations, PDF, HTML, Markdown,
reStructuredText and more.
one markup format to another, and a command-line tool that uses this
library :bookmark: :link:.
Command line spell checker.
Command line spell checker.
Open source grammar, style and
Analyses scientific LaTeX papers, suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences.
Markdown linter.
Linter for prose.
Markdown linter.
reStructuredText linter.
Pluggable linting tool for text
Spelling, grammar and
Free, open-source linter for
Naive linter for English
spell Checker.
and Markdown.
style checking on LaTeX documents.
prose built with speed and extensibility in mind.
prose.
Reusable minimalist examples.
Markdown-based templates for papers and RESUME/CVs, publishing with GitHub Pages.
Minimal
Clean academic pandoc LaTeX template.
example of a book based on R Markdown and bookdown.
Article provides an overview to a workflow that combines R Markdown (bookdown), Zotero (literature management), and Notion (note taking on research papers) to write academic papers.
Sustainable Authorship in Plain Text using Pandoc and Markdown.
Summary of the capabilities of Quarto, why to use it, and how it compares to R Markdown. Also contains tips for M1 Mac users on how to fix a common problem with reticulate.
Step-by-step guide on creating a complex pdf document, including text, figures, references, images, formatting, and more.
How to generate articles and presentations for scientific purposes.
example uses a custom nbconvert template and shows how to store your
notebooks with no output (for version control) while automatically executing
them before running bookbook, so that PDF and HTML versions include the
output.